D. Yarosh, R. S. Day, III, and others have shown that approximately 20% of human tumor lines and viral transformed lines are hypersensitive to alkylating agents due to an apparent absence of 06-alkylguanine DNA alkyltransferase (06AT); this phenotype has been designated mer-. This enzyme removes alkylation damage at the 0-6 position of guanine but not at other sites in DNA. Recently, a cDNA clone for a human 06AT has been isolated on the basis that it protects 06AT-deficient bacteria from certain alkylating agents (Tano, K, Shiota, S, Collier, J, Foote, RS, and Mitra, S. Isolation and structural characterization of a cDNA clone encoding the human DNA repair protein for 06-alkylguanine. Proc. Natl. Acad. Sci. USA 1990;87:686-690). Using oligonucleotides based on this sequence, we have isolated a full-length 06AT cDNA clone from a human liver library which we had constructed. Using this clone as a probe, we have found that 06AT mRNA was markedly reduced in all the mer- tumor cells lines examined. The level of 06AT mRNA varied by 10-fold in mer+ cell lines and correlated with known levels of the protein in particular cells. Our findings may have important implications in cancer therapy where agents such as BCNU are used. D. Yarosh has preliminary evidence that some brain tumors have no detectable 06AT activity. Determining which tumors are mer- and which mer+ tumors have low levels of 06AT mRNA and protein would probably be useful in planning chemotherapy. Efforts are underway to develop approaches to measure 06AT mRNA and protein levels in vivo. This has involved the production of recombinant 06AT protein and the development of antibodies using this recombinant protein.